9-5883409-G-T

Position:

• chr9-5883409-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000436015.6(KIAA2026):​c.*231-1734C>A variant causes a intron, NMD transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.977 in 151,098 control chromosomes in the GnomAD database, including 72,279 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.98 (72279 hom., cov: 26)
• Consequence: KIAA2026 ENST00000436015.6 intron, NMD_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.314

Genes affected

KIAA2026 (HGNC:23378): (bromodomain containing 10)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.986 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KIAA2026	XR_007061249.1	n.6353-1734C>A		intron_variant, non_coding_transcript_variant
KIAA2026	XR_007061250.1	n.6353-1734C>A		intron_variant, non_coding_transcript_variant
KIAA2026	XR_007061251.1	n.6241-1734C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KIAA2026	ENST00000436015.6	c.*231-1734C>A		intron_variant, NMD_transcript_variant		3		ENSP00000438370

Frequencies

GnomAD3 genomes AF: 0.977 AC: 147572 AN: 150982 Hom.: 72225 Cov.: 26

Gnomad AFR AF: 0.975

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.992

Gnomad ASJ AF: 0.988

Gnomad EAS AF: 0.795

Gnomad SAS AF: 0.926

Gnomad FIN AF: 0.980

Gnomad MID AF: 0.981

Gnomad NFE AF: 0.992

Gnomad OTH AF: 0.981

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.977 AC: 147685 AN: 151098 Hom.: 72279 Cov.: 26 AF XY: 0.975 AC XY: 71853 AN XY: 73698

Gnomad4 AFR AF: 0.975

Gnomad4 AMR AF: 0.992

Gnomad4 ASJ AF: 0.988

Gnomad4 EAS AF: 0.795

Gnomad4 SAS AF: 0.926

Gnomad4 FIN AF: 0.980

Gnomad4 NFE AF: 0.992

Gnomad4 OTH AF: 0.978

Alfa AF: 0.985 Hom.: 10828

Bravo AF: 0.979

Asia WGS AF: 0.859 AC: 2988 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.20
DANN	Benign	0.75

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10733517; hg19: chr9-5883409;